UPDATED | A pair of American flags normally atop the iconic towers of the Brooklyn Bridge mysteriously disappeared Tuesday morning, replaced by two white flags, the international symbol for surrender.

The white flags—which were bleached American flags—triggered an intense investigation by the New York Police Department

By early afternoon, police officers removed the two white flags and raised two American flags in their place.

At a news briefing, NYPD Deputy Commissioner of Intelligence John Miller said the stunt to remove the flags began after 3 a.m. Tuesday. The lights illuminating the flag near the Brooklyn side of the bridge flickered then went out, he said, followed by a similar scene on the Manhattan side of the bridge, according to surveillance footage.

Construction workers first noticed the flags missing this morning, and members of the NYPD’s Emergency Services Unit who inspected the scene found the bleached flags, measuring 20 feet by 11 feet. The lights had apparently been blocked with aluminum pans.

A white flag hangs over the Brooklyn Bridge Tuesday morning.

Keith Bedford for The Wall Street Journal

“There is some indication of a good deal of pre-operational planning,” Mr. Miller said, adding that he believes the incident didn’t have a “particularly nexus” to either terrorism or politics. He said the stunt was carried out by someone with construction or bridge experience.

The stunt was also no joke to Eric Adams, the Brooklyn borough president. On Tuesday afternoon, his office offered a $5,000 reward for information leading to the arrest of the person or people behind the flag prank. “I’m not laughing,” said Mr. Adams in a statement. “The public safety of our city is of paramount importance.”

The incident follows several other recent security breaches of landmarks, bridges and high-profile buildings in New York. In March, four men were arrested after videotaping a base jumping from atop One World Trade Center. The Brooklyn-based street artist known as Judith Supine was arrested this spring for installing one of his pieces atop the Ed Koch Queensboro Bridge in March; he has also hung works from the Manhattan and Williamsburg bridges. Last summer, a man rappelled off the side of the Brooklyn Bridge.

The iconic bridge is a favorite challenge among urban adventurers and pranksters alike. Unlike some of the New York’s other bridges, which can be scaled or reached by internal ladders, the top of the Brooklyn Bridge is accessed by walking along its steel cables, according to experts.

Those cables, about 18 inches in diameter, are reached most easily at the middle of the bridge and can be accessed from the promenade. So-called “suicide guards” are bypassed by a climb over the gates or the right tools. From there, it’s a long walk up the cables to a small metal ladder that leads to the top of the bridge’s tower, experts said.

“It’s not climbing a tightrope, it’s easier than that,” according to Sam Schwartz, president and chief executive of New York’s Sam Schwartz Engineering. Mr. Schwartz, a former New York City Traffic Commissioner, has climbed the bridge legitimately several times, he said. At least once a year, he estimated, someone summits the bridge as a prank or political statement.

“They probably videotaped it is my guess and we’ll see a YouTube of it,” said Mr. Schwartz.

Of course, getting atop the Brooklyn Bridge is also a major security issue, according to Micah Halpern, an expert on terrorism. “Someone has real serious egg on their face about this,” said Mr. Halpern. Like the twin towers at the World Trade Center, said Mr. Halpern, the Brooklyn Bridge is a symbol of New York and a “primary target” for terrorists. The bridge “doesn’t need to be destroyed to be a primary target, it just needs to be breached,” he said.

It’s unclear how the flags were replaced without any notice, since police cars are frequently stationed at the Brooklyn and Manhattan entrances to the bridge, and there are cameras located throughout the bridge, experts said.

Patrick Harris, 46, of the Upper West Side, was walking friends from France across the bridge as one of the new flags went up. The whole incident seemed “very strange” said Mr. Harris. “It surprises me that someone can get up there and do that. I’m amazed there’s not more security.”